1ZA3

The crystal structure of the YSd1 Fab bound to DR5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.230 

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This is version 1.3 of the entry. See complete history. 


Literature

Molecular recognition by a binary code.

Fellouse, F.A., Li, B., Compaan, D.M., Peden, A.A., Hymowitz, S.G., Sidhu, S.S.

(2005) J Mol Biol 348: 1153-1162

  • DOI: 10.1016/j.jmb.2005.03.041
  • Primary Citation of Related Structures:  
    1ZA3

  • PubMed Abstract: 

    • Functional antibodies were obtained from a library of antigen-binding sites generated by a binary code restricted to tyrosine and serine. An antibody raised against human vascular endothelial growth factor recognized the antigen with high affinity (K(D)= ...

    Functional antibodies were obtained from a library of antigen-binding sites generated by a binary code restricted to tyrosine and serine. An antibody raised against human vascular endothelial growth factor recognized the antigen with high affinity (K(D)=60 nM) and high specificity in cell-based assays. The crystal structure of another antigen binding fragment in complex with its antigen (human death receptor DR5) revealed the structural basis for this minimalist mode of molecular recognition. Natural antigen-binding sites are enriched for tyrosine and serine, and we show that these amino acid residues are intrinsically well suited for molecular recognition. Furthermore, these results demonstrate that molecular recognition can evolve from even the simplest chemical diversity.

    Organizational Affiliation: 

    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab-YSd1 light chain A, L213Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab-YSd1 heavy chain B, H236Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 10B R, S134Homo sapiensMutation(s): 0 
Gene Names: DR5, TNFRSF10B, KILLER, TRAILR2, TRICK2, ZTNFR9, UNQ160/PRO186
Find proteins for O14763 (Homo sapiens)
Explore O14763 
Go to UniProtKB:  O14763
NIH Common Fund Data Resources
PHAROS:  O14763
GTEx:  ENSG00000120889
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.230 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.059α = 90
b = 147.059β = 90
c = 144.947γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2014-02-05
    Changes: Source and taxonomy